diff --git a/.github/workflows/syntax-test.yml b/.github/workflows/syntax-test.yml index 4ef30d6..54dcfb6 100644 --- a/.github/workflows/syntax-test.yml +++ b/.github/workflows/syntax-test.yml @@ -16,10 +16,10 @@ jobs: if: github.event.pull_request.draft == false steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Configure Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.11' cache: 'pip' diff --git a/c/aguilar-2017.mmt b/c/aguilar-2017.mmt index 4083699..c45ce71 100644 --- a/c/aguilar-2017.mmt +++ b/c/aguilar-2017.mmt @@ -2,6 +2,7 @@ name: aguilar-2017 version: 20240904 mmt_authors: Michael Clerx +display_name: Aguilar et al., 2017 desc: """ Model of the human atrial action potential by Aguilar et al. [1], based on the model by Courtemanche et al. [2] and including the IKACh current diff --git a/c/akwaboah-2021-corrected.mmt b/c/akwaboah-2021-corrected.mmt index da8ecdb..0cd134a 100644 --- a/c/akwaboah-2021-corrected.mmt +++ b/c/akwaboah-2021-corrected.mmt @@ -1,7 +1,8 @@ [[model]] name: akwaboah-2021-corrected -version: 20240325 +version: 20240904 mmt_authors: Michael Clerx +display_name: Akwaboah et al., 2021 desc: """ Model of the hiPSC AP by Akwaboah et al [1], with corrections. diff --git a/c/akwaboah-2021-original.mmt b/c/akwaboah-2021-original.mmt index a3f7e92..1e8f3d0 100644 --- a/c/akwaboah-2021-original.mmt +++ b/c/akwaboah-2021-original.mmt @@ -1,7 +1,8 @@ [[model]] name: akwaboah-2021-original -version: 20240323 +version: 20240904 mmt_authors: Michael Clerx +display_name: Akwaboah et al., 2021 (uncorrected) desc: """ Model of the hiPSC AP by Akwaboah et al [1], matching the published code. diff --git a/c/bartolucci-2020.mmt b/c/bartolucci-2020.mmt index adcd13b..414e7d7 100644 --- a/c/bartolucci-2020.mmt +++ b/c/bartolucci-2020.mmt @@ -1,7 +1,8 @@ [[model]] name: bartolucci-2020 -version: 20240816 +version: 20240904 mmt_authors: Michael Clerx +display_name: Bartolucci et al., 2020 desc: """ The 2020 "BPS" model of the human ventricular AP by Bartolucci et al. [1]. diff --git a/c/beeler-1977.mmt b/c/beeler-1977.mmt index 96f8f10..c4efc8f 100644 --- a/c/beeler-1977.mmt +++ b/c/beeler-1977.mmt @@ -1,7 +1,8 @@ [[model]] name: beeler-1977 -version: 20230202 +version: 20240904 mmt_authors: Michael Clerx +display_name: Beeler & Reuter 1977 desc: """ The 1977 model of the AP in mammalian ventricular myocardial fibers by Beeler and Reuter [1]. diff --git a/c/carro-2011.mmt b/c/carro-2011.mmt index 495249d..cbb7b21 100644 --- a/c/carro-2011.mmt +++ b/c/carro-2011.mmt @@ -1,7 +1,8 @@ [[model]] name: carro-2011 -version: 20240903 +version: 20240904 mmt_authors: Michael Clerx +display_name: Carro et al., 2011 desc: """ The 2011 model of the human ventricular AP by Carro et al. [1], based on the model by Grandi et al. [2]. diff --git a/c/courtemanche-1998.mmt b/c/courtemanche-1998.mmt index 126f80c..1515aaa 100644 --- a/c/courtemanche-1998.mmt +++ b/c/courtemanche-1998.mmt @@ -2,6 +2,7 @@ name: courtemanche-1998 version: 20240904 mmt_authors: Michael Clerx +display_name: Courtemanche et al., 1998 desc: """ Model of the human atrial action potential by Courtemanche et al. [1]. diff --git a/c/decker-2009.mmt b/c/decker-2009.mmt index dedc54d..08be6ba 100644 --- a/c/decker-2009.mmt +++ b/c/decker-2009.mmt @@ -1,7 +1,8 @@ [[model]] name: decker-2009 -version: 20230202 +version: 20240904 mmt_authors: Michael Clerx +display_name: Decker et al., 2009 desc: """ The 2009 model of the canine (left) ventricular AP by Decker et al. [1]. diff --git a/c/ellinwood-2017.mmt b/c/ellinwood-2017.mmt index 8013cfb..5d6fc8d 100644 --- a/c/ellinwood-2017.mmt +++ b/c/ellinwood-2017.mmt @@ -2,6 +2,7 @@ name: ellinwood-2017 version: 20240904 mmt_authors: Michael Clerx +display_name: Ellinwood et al., 2017 desc: """ The 2017 model of the human atrial AP by Ellinwood et al. [1, 2]. Based on the adaptation of the Grandi model [3] by Morotti et al. [4]. diff --git a/c/gokhale-2017-23.mmt b/c/gokhale-2017-23.mmt index 2890808..c25f354 100644 --- a/c/gokhale-2017-23.mmt +++ b/c/gokhale-2017-23.mmt @@ -1,7 +1,8 @@ [[model]] name: gokhale-2017-23 -version: 20230503 +version: 20240904 mmt_authors: Michael Clerx +display_name: Gokhale et al., 2017 (23C) desc: """ The 2017 model of the ex293 AP by Gokhale et al. [1], 23 degrees C version. diff --git a/c/gokhale-2017-35.mmt b/c/gokhale-2017-35.mmt index 2686d82..7956cf4 100644 --- a/c/gokhale-2017-35.mmt +++ b/c/gokhale-2017-35.mmt @@ -1,19 +1,20 @@ [[model]] -name: gokhale-2017-23 -version: 20230503 +name: gokhale-2017-35 +version: 20240904 mmt_authors: Michael Clerx +display_name: Gokhale et al., 2017 (35C) desc: """ The 2017 model of the ex293 AP by Gokhale et al. [1], 35 degrees C version. The Nav1.5 and Kir2.1 currents in the 23C model are based on the data from [2], while endogeneous INa and IK were fit to [3] and [4] respectively. All currents in the 35 degrees model were temperature-shifted, sometimes - using literature data on temperature effects, sometimes by fitting to + using literature data on temperature effects, sometimes by fitting to tissue data (including conduction velocity). - + The formulation of the Nav1.5 current is based on the model by Lindblad et al. [5], the endogenous INa is a class Hodgkin-Huxley m^3*h form, and the - endogenous IK current formulation is based on the IKs equations in [6]. + endogenous IK current formulation is based on the IKs equations in [6]. This implementation is based on the equations given in the paper and supplement [1]. To avoid overshadowing the sodium current, the stimulus @@ -24,7 +25,7 @@ desc: """ units for conductances were changed from [mS/cm^2] to [nS/pF] (thereby removing the assumption that the specific membrane capacity is exactly 1 uF/cm^2). - + The implementation was verified by recreating parts of figures 1 and 2, which could partly be achieved (some information on monodomain parameters and the exact stimulus and voltage-clamp protocols is missing). In @@ -36,21 +37,21 @@ desc: """ Variability for Paired Computational-Experimental Studies. PLOS Computational Biology. 13(1): e1005342. https://doi.org/10.1371/journal.pcbi.1005342 - + [2] Kirkton, R. D., and Bursac, N. (2011) Engineering biosynthetic excitable tissues from unexcitable cells for electrophysiological and cell therapy studies. Nature communications 2:300 https://doi.org/10.1038/ncomms1302 - - [3] He, B., and Soderlund, D. M. (2017) Human embryonic kidney (HEK293) - cells express endogenous voltage-gated sodium currents and Nav1.7 + + [3] He, B., and Soderlund, D. M. (2017) Human embryonic kidney (HEK293) + cells express endogenous voltage-gated sodium currents and Nav1.7 sodium channels. Neuroscience Letters 469:268-272. http://doi.org/10.1016/j.neulet.2009.12.012 [4] Yu, S. P., and Kerchner, G. A. (1998) Endogenous voltage-gated potassium channels in human embryonic kidney (HEK293) cells. Journal of Neuroscience Research, 52:612-617. - + [5] Lindblad, D.S., Murphey, C.R., Clark, J.W., and Giles, W.G. (1996) A model of the action potential and underlying membrane currents in a rabbit atrial cell. American Journal of Physiology, 271, H1666-H1691. @@ -225,7 +226,7 @@ use membrane.V, rev.EK dot(b) = (inf - b) / tau inf = 1 / (1 + exp((V + 24.96 [mV]) / -36.58 [mV])) tau = 0.584 [ms] - in [ms] + in [ms] g = 0.1332 [nS/pF] in [nS/pF] IKwt = g * b^2 * (V - EK) diff --git a/c/grandi-2010.mmt b/c/grandi-2010.mmt index 2f76878..4a06585 100644 --- a/c/grandi-2010.mmt +++ b/c/grandi-2010.mmt @@ -1,7 +1,8 @@ [[model]] name: grandi-2010 -version: 20240903 +version: 20240904 mmt_authors: Michael Clerx +display_name: Grandi et al., 2010 desc: """ The 2010 model of the human ventricular AP by Grandi et al. [1]. diff --git a/c/grandi-2011.mmt b/c/grandi-2011.mmt index 40ec4a5..4f593a4 100644 --- a/c/grandi-2011.mmt +++ b/c/grandi-2011.mmt @@ -1,7 +1,8 @@ [[model]] name: grandi-2011 -version: 20240903 +version: 20240904 mmt_authors: Michael Clerx +display_name: Grandi-Pandit-Voigt et al., 2011 desc: """ The 2011 model of the human atrial AP by Grandi, Pandit, Voigt et al. [1]. @@ -9,7 +10,7 @@ desc: """ first author [2]. This implementation is based on the original Matlab code provided on the - Grandi lab website [3]. It was checked against the original code + Grandi lab website [3]. It was checked against the original code numerically by comparing the calculated derivatives. The stimulus was set to 0.5 ms and approximately twice the threshold value diff --git a/c/iyer-2004.mmt b/c/iyer-2004.mmt index 043a0c0..1cbf376 100644 --- a/c/iyer-2004.mmt +++ b/c/iyer-2004.mmt @@ -2,6 +2,7 @@ name: iyer-2004 version: 20240904 mmt_authors: Michael Clerx +display_name: Iyer et al., 2004 desc: """ The 2004 model of the human left-ventricular AP by Iyer et al. [1]. @@ -12,7 +13,7 @@ desc: """ The formulation for ical.y.tau used in this file is the one from the code, which differs slightly from the version in the paper (which is used in the updated CellML file). - + The stimulus was set to 0.5ms and approximately twice the minimum level for depolarisation. diff --git a/c/kernik-2019.mmt b/c/kernik-2019.mmt index 62ea7be..6315b1e 100644 --- a/c/kernik-2019.mmt +++ b/c/kernik-2019.mmt @@ -1,7 +1,8 @@ [[model]] name: kernik-2019 -version: 20230202 +version: 20240904 mmt_authors: Michael Clerx +display_name: Kernik et al., 2019 desc: """ The 2019 model of induced pluripotent stem-cell derived cardiomyocyte AP by Kernik et al. [1]. diff --git a/c/koivumaki-2011.mmt b/c/koivumaki-2011.mmt index 9a36cf5..d996568 100644 --- a/c/koivumaki-2011.mmt +++ b/c/koivumaki-2011.mmt @@ -1,9 +1,10 @@ [[model]] name: koivumaki-2011 -version: 20240903 +version: 20240904 mmt_authors: Michael Clerx +display_name: Koivumäki et al., 2011 desc: """ - The 2011 model of the human atrial AP by Koivumaki et al. [1], based on the + The 2011 model of the human atrial AP by Koivumäki et al. [1], based on the earlier model by Nygren et al. [2]. The stimulus was set to 0.5 ms and approximately twice the threshold for @@ -14,7 +15,7 @@ desc: """ calculated derivatives. The code can be run to produce an AP similar to that seen in the original paper. - [1] Koivumaki, J. T, Korhonen, T., & Tavi P. (2011). Impact of Sarcoplasmic + [1] Koivumäki, J. T, Korhonen, T., & Tavi P. (2011). Impact of Sarcoplasmic Reticulum Calcium Release on Calcium Dynamics and Action Potential Morphology in Human Atrial Myocytes: A Computational Study. PLOS Computational Biology, 7(1), e1001067. diff --git a/c/livshitz-2007.mmt b/c/livshitz-2007.mmt index 9fb65c7..40b226a 100644 --- a/c/livshitz-2007.mmt +++ b/c/livshitz-2007.mmt @@ -1,7 +1,8 @@ [[model]] name: livshitz-2007 -version: 20230202 +version: 20240904 mmt_authors: Michael Clerx +display_name: Livshitz & Rudy 2007 desc: """ The 2007 update by Livshitz & Rudy [1] of the canine ventricular AP model by Hund & Rudy [2]. diff --git a/c/maleckar-2009.mmt b/c/maleckar-2009.mmt index b37d5a3..db5989e 100644 --- a/c/maleckar-2009.mmt +++ b/c/maleckar-2009.mmt @@ -2,6 +2,7 @@ name: maleckar-2009 version: 20240904 mmt_authors: Michael Clerx +display_name: Maleckar et al., 2009 desc: """ Model of the human atrial action potential by Maleckar et al. [1], based on the Nygren et al. [2]. The model contains an IKACh current which is diff --git a/c/ni-2017.mmt b/c/ni-2017.mmt index ad69f5e..13d0014 100644 --- a/c/ni-2017.mmt +++ b/c/ni-2017.mmt @@ -2,6 +2,7 @@ name: ni-2017 version: 20240904 mmt_authors: Michael Clerx +display_name: Ni et al., 2017 desc: """ The 2017 model of the human atrial AP by Ni et al. [1]. diff --git a/c/noble-1962.mmt b/c/noble-1962.mmt index cdd3be0..c9c997f 100644 --- a/c/noble-1962.mmt +++ b/c/noble-1962.mmt @@ -1,11 +1,12 @@ [[model]] name: noble-1962 -version: 20230202 +version: 20240904 mmt_authors: Michael Clerx +display_name: Noble, 1962 desc: """ The 1962 model of the AP in Purkinje fibers by Denis Noble [1]. - Adapted from CellML version. + Adapted from the CellML version by Catherine LLoyd. References : @@ -14,44 +15,8 @@ desc: """ of Physiology, 160(2), 317-352. https://doi.org/10.1113/jphysiol.1962.sp006849 - Original CellML metadata follows below: - --------------------------------------- + [2] https://models.physiomeproject.org/e/2a6 - Noble Purkinje Fibre Model 1962 - Catherine Lloyd - Auckland Bioengineering Institute, The University of Auckland - - Model Status - This CellML model runs in COR, JSim and OpenCell to recreate the published - results. The units have been checked and they are consistent. - - Model Structure - - In 1962, Denis Noble published one of the first mathematical models of a - cardiac cell. By adapting the equations of the original Hodgkin-Huxley - squid axon model (1952), Noble described the long lasting action and - pace-maker potentials of the Purkinje fibres of the heart. The - potassium-current equations differ from those of Hodgkin and Huxley in that - the potassium ions are assumed to flow through two types of channel in the - membrane. By contrast, the sodium current equations are very similar to - those of Hodgkin and Huxley. The main failure of the Noble (1962) model is - that it only includes one voltage gated inward current, INa. Calcium - currents had not yet been discovered, but there was a clue in the model - that something was missing. The only way the model could be made to work - was to greatly extend the voltage range of the sodium current by reducing - the voltage dependence of the sodium activation process. In effect the - sodium current was made to serve the function of both the sodium and the - calcium channels as far as the plateau is concerned. There was a clear - experimental prediction: either sodium channels in the heart are - quantitatively different from those in neurons, or other inward - current-carrying channels must exist. Both predictions are correct. - - The original paper reference is cited below: - - A Modification of the Hodgkin-Huxley Equations Applicable to Purkinje Fibre - Action and Pacemaker Potentials, Noble, D. 1962 - Journal of Physiology, 160, 317-352. - PubMed ID: 14480151 """ # Initial values membrane.V = -87.0 diff --git a/c/nygren-1998.mmt b/c/nygren-1998.mmt index 0f1f258..bb22dfb 100644 --- a/c/nygren-1998.mmt +++ b/c/nygren-1998.mmt @@ -2,6 +2,7 @@ name: nygren-1998 version: 20240904 mmt_authors: Michael Clerx +display_name: Nygren et al., 1998 desc: """ Model of the human atrial action potential by Nygren et al. [1, 2], based in part on the earlier rabbit atrial model by Lindblad et al. [3]. diff --git a/c/ohara-cipa-v1-2017.mmt b/c/ohara-cipa-v1-2017.mmt index aae544a..95673ec 100644 --- a/c/ohara-cipa-v1-2017.mmt +++ b/c/ohara-cipa-v1-2017.mmt @@ -2,7 +2,7 @@ name: dutta-2017 version: 20240904 mmt_authors: Michael Clerx -display_name: O'Hara-CiPA-v1, 2017 +display_name: Dutta et al., 2017 desc: """ The 2017 "CiPA v1" update [1, 2, 3] of the O'Hara et al. model of the human ventricular AP [4]. diff --git a/c/paci-2013-ventricular-vs.mmt b/c/paci-2013-ventricular-vs.mmt index 09c3e79..a3b2ce7 100644 --- a/c/paci-2013-ventricular-vs.mmt +++ b/c/paci-2013-ventricular-vs.mmt @@ -1,7 +1,8 @@ [[model]] name: paci-2013-vs -version: 20230202 +version: 20240904 mmt_authors: Michael Clerx +display_name: Paci et al., 2013 (ventricular) desc: """ The 2013 model of the hiPSC AP by Paci et al. [1], ventricular version, but with the original units of volts and seconds. diff --git a/c/priebe-1998.mmt b/c/priebe-1998.mmt index 4e483f1..f0051ac 100644 --- a/c/priebe-1998.mmt +++ b/c/priebe-1998.mmt @@ -1,12 +1,13 @@ [[model]] name: priebe-1998 -version: 20240903 +version: 20240904 mmt_authors: Michael Clerx +display_name: Priebe & Beuckelmann, 1998 desc: """ The 1998 model of the human ventricular AP by Priebe and Beuckelmann [1]. Adapted from the CellML implementation by Catherline Lloyd [2]. - + The stimulus duration was set to 0.5ms, and the amplitude was set to approximately twice the minimum needed to elicit three successive APs. diff --git a/c/sampson-2010.mmt b/c/sampson-2010.mmt index a37d300..4c5df2b 100644 --- a/c/sampson-2010.mmt +++ b/c/sampson-2010.mmt @@ -2,6 +2,7 @@ name: sampson-2010 version: 20240904 mmt_authors: Michael Clerx +display_name: Sampson et al., 2024 desc: """ The 2010 model of the human Purkinje cell AP by Sampson et al. [1]. diff --git a/c/tomek-2020.mmt b/c/tomek-2020.mmt index 851b892..11b36e9 100644 --- a/c/tomek-2020.mmt +++ b/c/tomek-2020.mmt @@ -1,7 +1,8 @@ [[model]] name: tomek-2020 -mmt_authors: Michael Clerx version: 20240904 +mmt_authors: Michael Clerx +display_name: Tomek et al., 2024 desc: """ The Tomek et al. "ToRORd-dynCL" model of the human ventricular action potential [1], based on the earlier model without dynamic chloride [2], diff --git a/c/trovato-2020.mmt b/c/trovato-2020.mmt index 7a3dec8..8856e33 100644 --- a/c/trovato-2020.mmt +++ b/c/trovato-2020.mmt @@ -2,6 +2,7 @@ name: trovato-2020 version: 20240904 mmt_authors: Michael Clerx +display_name: Trovato et al., 2020 desc: """ The 2020 model of the human Purkinje cell AP by Trovato et al. [1]. @@ -14,7 +15,7 @@ desc: """ implementation was verified by comparing the calculated derivatives to the original CellML and seeing that they matched to within machine precision. After this verification, a minor correction to INaK was applied [6]. - + The stimulus was set to approximately twice the minimum needed to create three successive APs when pacing at 1Hz with a 0.5ms stimulus. diff --git a/c/voigt-2013.mmt b/c/voigt-2013.mmt index 58fefd2..f514c90 100644 --- a/c/voigt-2013.mmt +++ b/c/voigt-2013.mmt @@ -2,6 +2,7 @@ name: voigt-2013 version: 20240904 mmt_authors: Henry Sutanto, Jordi Heijman, Michael Clerx +display_name: Voigt-Heijman et al., 2013 desc: """ The 2013 model of the human atrial AP by Voigt & Heijman et al. [1]. diff --git a/g/logistic.mmt b/g/logistic.mmt index 971e74b..47af6a4 100644 --- a/g/logistic.mmt +++ b/g/logistic.mmt @@ -1,7 +1,8 @@ [[model]] name: logistic -version: 20230202 +version: 20240904 mmt_authors: Michael Clerx +display_name: Logistic growth model desc: """ Logistic growth model, see e.g. [1]. diff --git a/g/lotka-volterra.mmt b/g/lotka-volterra.mmt index 477ed36..da6c17d 100644 --- a/g/lotka-volterra.mmt +++ b/g/lotka-volterra.mmt @@ -1,7 +1,8 @@ [[model]] name: lotka-volterra -version: 20230202 +version: 20240904 mmt_authors: Michael Clerx +display_name: Lotka-Volterra predator-prey model desc: """ Lotka-Volterra predator-prey equations, see e.g. [1]. diff --git a/test.py b/test.py index 0135520..9bc7eb1 100755 --- a/test.py +++ b/test.py @@ -75,6 +75,7 @@ def test(path): 'mmt_authors', 'version', 'desc', + 'display_name', ] for tag in tags: if tag not in m.meta: